yeah. its easy if u have only 2 objects but not with 6.
i think its buggy. only at 3rd time it worked correctly.
and i had to manually delete the cutter
You wrote your question in the title…do you mean like this?
I tried to replicate your issue, but was not able. For me, it seems to react as expected.
But with the subtracted bodies that are flush to the remaining ones, it can be difficult to select the right body with the right action. It happens to me during the first video I did: I thought I had replicated your issue and captured it on video, but when I played it back, actually one body that was supposed to be selected as “+” was in fact selected as “-”. I would have swear it was correctly selected but the video proves me it was not 
So I dit the video again and upload it, showing the behaviour for the 4 different modes of subtraction.
At least with the 5.92 version, I can’t replicate your problem.
Seen flaws like this as well, but… I agree, it is not a perfect toool Subtraction.
I would like to see a better tool for analysing my sketches and definitely a way of sorting out WHICH end-point I’m activating when trying to move points “stacked” on others. Just ridiculous to separate at times, no doubt something to improve on.(topic raised before)
Some sort of confirmation or like in Onshape changing color, from blue to black once lines or curves are “OK”(plain english) would be nice as well!